In her first full broadcast interview since leaving Brussels, Prof Anne Glover defended her stance on GMOs.
And she denied reports that she was "sacked", saying she intended to leave.
She told the BBC programme Hardtalk that criticism from environmental groups over her role was unjustified.
Prof Anne Glover, a former chief scientific adviser to the Scottish government, was accused by NGOs in July of presenting "one-sided, partial opinions" in the debate over GM crops.
She had argued opposition to GMOs was "a form of madness".
In a letter to the incoming President of the European Commission, Jean-Claude Juncker, NGOs said her views about the safety of GMOs misrepresented the diversity of opinion among scientists.
They called for the newly created post of chief scientific adviser to the European Commission to be scrapped, saying it was "unaccountable, intransparent and controversial".
Defending her position on GM, Prof Glover told the BBC: "I am not a strong advocate of GM crops.
"What I am saying is that the technology used to generate GM crops is safe - that is what the scientific consensus is.
"Now it is up to individual countries, nations, to decide whether or not they want to use that technology.
"But to keep on saying that we don't have enough evidence or that there might be some kind of unforeseen negative consequence of using this technology, that is simply not the case."
She said she spoke out because those opposed to GM crop did so based on ideology not evidence.
And while "disappointed" by the letter, it paled into significance compared with "warm and very positive letters of support from scientists" and others she had received.
Prof Glover, a professor of microbiology at Aberdeen University, said her role was tied to the former EC president, José Manuel Barroso, and she did not want to stay on.
But she said before leaving she had asked for a meeting with Mr Juncker, which never took place.
Many scientists have called for the role to continue, saying it is vital to ensure EU policies on important issues are underpinned by scientific evidence.
Source: BBC